Thymosin ␣ 1 (T␣ 1 ) and thymosin T␣ 11 (T␣ 11 ) are polypeptides with immunoregulatory properties first isolated from thymic extracts, corresponding to the first 28 and 35 amino acid residues, respectively, of prothymosin ␣ (ProT␣), a protein involved in chromatin remodeling. It has been widely supposed that these polypeptides are not natural products of the in vivo processing of ProT␣, since neither was found in extracts in which proteolysis was prevented. Here we show that a lysosomal asparaginyl endopeptidase is able to process ProT␣ to generate T␣ 1 and T␣ 11 . In view of its catalytic properties and structural and immunological analyses, this protease was identified as mammalian legumain. It selectively cleaves some of the asparaginylglycine residues in the ProT␣ sequence; specifically, Asn 28 -Gly 29 and Asn 35 -Gly 36 residues are cleaved with similar efficiency in vitro to generate T␣ 1 and T␣ 11 , respectively. By contrast T␣ 1 is the main product detected in vivo, free in the cytosol, at concentrations similar to that of ProT␣. The data here reported demonstrate that T␣ 1 is not an artifact but rather is naturally present in diverse mammalian tissues and raise the possibility that it has a functional role.